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[新手求助] Help: Suggestion for gaussian calculation setup involving nanoparticles and DNA

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发表于 2020-11-13 05:00:01 | 显示全部楼层 |阅读模式
Greetings, I want to use gaussian to see the interaction between DNA and nanoparticles(NPs) of gold and silver, for these, I was thinking on calculate the binding energy between the DNA and the NPs and also make a cytosine(C)-guanine(G) and put one NPs in different places and measure the binding energy between C-G. For this, the cluster of gold and silver were made by putting some atoms and do an optimization using Lanl2dz, the C-G was optimized using B3LYP.

I'm not pretty sure how to calculate the energy between the C-G and the NPs, maybe using Gen keyword or even if this kind of approximation makes sense, so I open to suggestions, changes in calculation, improvement, advice, etc.

Thanks in advance.

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发表于 2020-11-13 06:52:00 | 显示全部楼层
You can refer to the binding energy calculation for benzene - Ag surface described in this post: http://bbs.keinsci.com/thread-16532-1-1.html
The difference is that you may want to use a spherical metal cluster instead of a finite slab model.

The binding energy can be calculated as E(GC-NP) - E(GC) - E(NP). For optimization purpose, Lanl2DZ for Au/Ag and 6-31G* for C-G is acceptable, however for evaluating binding energy, better basis set should be used, for example, SDD for Au/Ag and 6-311+G** for C-G, and its is best to consider Counterpoise correction. The recommended DFT functional for this case is PBE0-D3(BJ). B3LYP without dispersion correction should never be used for evaluating the binding energy because it is well known that B3LYP completely fails to represent dispersion effect.
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发表于 2020-11-13 10:50:23 | 显示全部楼层
Please note that LANL2DZ is a basis set while B3LYP is a functional. Every calculation requires both a functional and a basis set, so sentences like "do an optimization using Lanl2dz, the C-G was optimized using B3LYP" don't really make sense. Functionals are global, so one cannot specify different functionals for different atoms, but it is possible to assign different basis sets to different atoms.

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 楼主| 发表于 2020-11-21 00:40:51 | 显示全部楼层
sobereva 发表于 2020-11-12 17:52
You can refer to the binding energy calculation for benzene - Ag surface described in this post: htt ...

Thanks, I will try it and let you know, any suggestion to create the spherical metal cluster?

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 楼主| 发表于 2020-11-21 00:46:56 | 显示全部楼层
wzkchem5 发表于 2020-11-12 21:50
Please note that LANL2DZ is a basis set while B3LYP is a functional. Every calculation requires both ...

Thanks, you're right, I apologize I check and we use pbepbe/def2sv for both, the C-G and the metal cluster.

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发表于 7 天前 | 显示全部楼层
rpestana94 发表于 2020-11-21 00:46
Thanks, you're right, I apologize I check and we use pbepbe/def2sv for both, the C-G and the metal ...

def2sv is too small a basis set to be of publication quality, because it doesn't have any polarization functions. If you want to stick to the def2 series, you should use at least def2svpp.

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发表于 前天 11:08 | 显示全部楼层
rpestana94 发表于 2020-11-21 00:40
Thanks, I will try it and let you know, any suggestion to create the spherical metal cluster?

You can use VMD program to dig out a spherical cluster from supercell of metal
北京科音自然科学研究中心http://www.keinsci.com  致力于计算化学的发展和传播,长期开办最高水准的各种量子化学、分子动力学、波函数分析与Multiwfn程序等主题的培训,是提升计算化学研究水平的最佳选择。欢迎加入“北京科音”公众号获取培训最新消息和计算化学资讯!培训相关信息见《北京科音办的培训班FAQ》(http://bbs.keinsci.com/thread-5098-1-1.html)。
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